1.) Good documentation, good programming style
2.) Looks easier to use, but is not as elegant as other autoloaders. Takes a brute force approach. This is fine with me as use of this autoloader will be optional.
3.) Nice use of SPL interfaces
4.) Class variables require a scope declaration (public/private/protected)
5.) I'm not sure if calling immediately executable code in a file is still allowed in PEAR. IF not allowed, it would be relatively easy to put the default class registrations in the class constructors instead.
6.) Package directory structure should follow the PEAR conventions:
PHP/
__Autoloader.php
__Autoloader/
____Abstract.php
____Internal.php
____Exception.php
____Exception/
______GuessPathFailed.php
______..etc..
____API.php
____API/
______Old.php
7.) Memcached and APC index backends would be a good idea.
8.) Use single or double quotes, not both.
9.) Like Christian said, the GPL is not suitable for PEAR packages. All PEAR packages need to remain usable by commercial applications to prevent confusion. Consider the LGPL or a more permissive license like MIT, Apache or BSD.